{"status":"OK","data":{"id":217620,"identifier":"9Q0FVO","persistentUrl":"https://doi.org/10.34894/9Q0FVO","protocol":"doi","authority":"10.34894","separator":"/","publisher":"DataverseNL","publicationDate":"2022-04-19","storageIdentifier":"surf://10.34894/9Q0FVO","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9732,"datasetType":"dataset","locks":[],"latestVersion":{"id":20961,"datasetId":217620,"datasetPersistentId":"doi:10.34894/9Q0FVO","datasetType":"dataset","storageIdentifier":"surf://10.34894/9Q0FVO","versionNumber":2,"internalVersionNumber":61,"versionMinorNumber":0,"versionState":"RELEASED","latestVersionPublishingState":"RELEASED","deaccessionLink":"","lastUpdateTime":"2023-01-10T17:02:46Z","releaseTime":"2023-01-10T17:02:46Z","createTime":"2022-06-04T06:56:10Z","publicationDate":"2022-04-19","citationDate":"2022-04-19","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9732,"termsOfUse":"The standard Data Sharing Agreement (DSA) of the UMC Utrecht must be signed without adjustments. This DSA is in compliance with Dutch law. No costs are involved","confidentialityDeclaration":"no","specialPermissions":"To obtain access to the data, a request form\nhas to be completed. In addition to a completed request form, a Data Sharing Agreement\n(DSA) in line with GDPR regulations and/or a Research Collaboration Agreement (RCA) should\nbe signed before data is shared. Only data requests in line with the Terms of Use will be\ntaken into consideration.","restrictions":"See Data Sharing Agreement","citationRequirements":"See Data Sharing Agreement","conditions":"To access and use the dataset please read the Terms of Use and the Terms of Access.\n","disclaimer":"See Data Sharing Agreement.","termsOfAccess":"The data is not available for download directly via DataverseNL. Data is available on request by completing the request form. Only data requests in line with the Terms of Use will be taken into consideration. In addition to a completed request form, the Data Sharing Agreement (DSA) in line with GDPR regulations and/or the Research Collaboration Agreement (RCA) should be signed before data is shared. If a data request is approved, the data will be delivered in a safe and secure manner. By signing the DSA and/or RCA and\naccessing the Materials, the recipient represents his/her acceptance of the Terms of Use.","availabilityStatus":"The data is not available for download directly via DataverseNL but is available on request if the request is compliant with the Terms of Access","contactForAccess":"Please fill out the request form.","fileAccessRequest":true,"metadataBlocks":{"citation":{"displayName":"Citation Metadata","name":"citation","fields":[{"typeName":"title","multiple":false,"typeClass":"primitive","value":"Data and R Scripts for: \"Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis\""},{"typeName":"subtitle","multiple":false,"typeClass":"primitive","value":"CD1c+ cDC2 RNA seq in non-infectious uveitis"},{"typeName":"author","multiple":true,"typeClass":"compound","value":[{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Jonas J.W. Kuiper"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0002-5370-6395"}}]},{"typeName":"datasetContact","multiple":true,"typeClass":"compound","value":[{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"data management"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"Jonas J.W. Kuiper"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}}]},{"typeName":"dsDescription","multiple":true,"typeClass":"compound","value":[{"dsDescriptionValue":{"typeName":"dsDescriptionValue","multiple":false,"typeClass":"primitive","value":"This dataset contains the processed RNA sequencing data of purified CD1c-positive conventional type 2 dendritic cells (CD1c+ cDC2s), functional enrichment analysis, manual and automatic gating data of (i.e., flowSOM) flow cytometry, and multiplex cytokine analyses as outlined in Hiddingh et al. 2022 \"Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis
see preprint on BioRxiv\n
\nData are from two cohorts (cohort I, n=36, and cohort II, n=42) of in total 51 patients with non-infectious uveitis (HLA-B27-positive acute anterior uveitis, idiopathic intermediate uveitis, HLA-A29-positive Birdshot Uveitis (Birdshot chorioretinopathy), and 27 sex/age-matched healthy controls without ocular inflammatory disease).

\nAll raw sequencing data are available at NCBI SRA under the accession number:
\n\n
  • GSE195501 (FACS-sorted cohort I).
    • \n
  • GSE194060 (MACS-sorted cohort II).
    • \n
    \nThis dataverseNL dataset contains additional raw, processed, and metadata (see readme file and reproducible R notebooks (R script and Image) used for the analysis in the manuscript:

    \n
    \n
    R scripts (markdown + R image) with step-by-step analyses
    \n\n\n
    Experimental data
    \n\n\n\n
    Other transcriptomic data used in the R scripts (above)
    \n
    "},"dsDescriptionDate":{"typeName":"dsDescriptionDate","multiple":false,"typeClass":"primitive","value":"2022-01-10"}}]},{"typeName":"subject","multiple":true,"typeClass":"controlledVocabulary","value":["Medicine, Health and Life Sciences"]},{"typeName":"keyword","multiple":true,"typeClass":"compound","value":[{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Uveitis"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"RNA-sequencing"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Dendritic cells"}}]},{"typeName":"publication","multiple":true,"typeClass":"compound","value":[{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis.\n

    \nS. Hiddingh, A. Pandit, F.H. Verhagen, R. Rijken, N. H. Servaas, C.G.K. Wichers, N.H. ten Dam-van Loon, S.M. Imhof, T.R.D.J. Radstake, J.H. de Boer, J.J.W. Kuiper* 2022

    \n*) Corresponding author\n

    \nBioRxiv"},"publicationIDType":{"typeName":"publicationIDType","multiple":false,"typeClass":"controlledVocabulary","value":"url"},"publicationURL":{"typeName":"publicationURL","multiple":false,"typeClass":"primitive","value":"https://www.biorxiv.org/content/10.1101/2021.11.16.468816v4"}}]},{"typeName":"notesText","multiple":false,"typeClass":"primitive","value":"Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis\n

    \nBackground:Type I interferons (IFNs) promote the expansion of subsets of CD1c+ conventional dendritic cells (CD1c+ DCs), but the molecular basis of CD1c+ DCs involvement in conditions not associated without elevated type I IFNs remains unclear.\n

    \nMethods: We analyzed CD1c+ DCs from two cohorts of non-infectious uveitis patients and healthy donors using RNA-sequencing followed by high-dimensional flow cytometry to characterize the CD1c+ DC populations.

    \nResults: We report that the CD1c+ DCs pool from patients with non-infectious uveitis is skewed towards a gene module with the chemokine receptor CX3CR1 as the key hub gene. We confirmed these results in an independent case-control cohort and show that the disease-associated gene module is not mediated by type I IFNs. An analysis of peripheral blood using flow cytometry revealed that CX3CR1+ DC3s were diminished, whereas CX3CR1- DC3s were not. Stimulated CX3CR1+ DC3s secrete high levels of inflammatory cytokines, including TNF-alpha, and CX3CR1+ DC3-like cells can be detected in inflamed eyes of patients.

    Conclusion: These results show that CX3CR1+ DC3s are implicated in non-infectious uveitis and can secrete proinflammatory mediators implicated in its pathophysiology."},{"typeName":"language","multiple":true,"typeClass":"controlledVocabulary","value":["English"]},{"typeName":"productionPlace","multiple":true,"typeClass":"primitive","value":["University Medical Center Utrecht"]},{"typeName":"grantNumber","multiple":true,"typeClass":"compound","value":[{"grantNumberAgency":{"typeName":"grantNumberAgency","multiple":false,"typeClass":"primitive","value":"Uitzicht"},"grantNumberValue":{"typeName":"grantNumberValue","multiple":false,"typeClass":"primitive","value":"2014-4/2015-5"}}]},{"typeName":"depositor","multiple":false,"typeClass":"primitive","value":"Kuiper, Jonas"},{"typeName":"dateOfDeposit","multiple":false,"typeClass":"primitive","value":"2022-01-03"}]},"dansDataVaultMetadata":{"displayName":"Data Vault 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